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Dear Steve, I don't make sure whether using the value p>0.95 to threshold the _tfce_p_tstat is rationable. If so, I can find some significant results, which still are uncorrected. Thanks. 2008/11/25 Steve Smith <[log in to unmask]> > Hi - although this is sometimes done in reporting studies, I'm afraid it's > not really valid as a way of controlling for multiple comparisons across > voxels. If you didn't find any significant clusters, have you tried using > TFCE (i.e. the --T2 option)? If none of these work, the only other way to > 'boost' significance is to limit the search space (randomise mask) to only > those areas of the brain/skeleton that you honestly are considering looking > for results in. > > Cheers. > > > > On 25 Nov 2008, at 09:08, liang wang wrote: > > Dear Steve, >> >> Thanks for your help. >> At the initial stage, I attempted to use 0.95 to threshold the >> _tfce_corrp_tstat_ or _vox_corrp_tstat images. however, no significant >> results could survive in this situation. Accordingly, I just used more >> conservative value (0.995) to threshold the _vox_p image and got an >> uncorrected image. As an additional safeguard against false positives, we >> only retained clusters larger than 10 voxels in size. Do you think if this >> step is rationable. >> >> Many thanks, >> Liang Wang >> >> >> 2008/11/25 Steve Smith <[log in to unmask]> >> Hi, >> >> Note that 0.995 corresponds to P<0.005, corrected, i.e. more conservative >> than most people use. >> >> You can use the "Cluster" program and the --osize option to get an image >> of cluster sizes output, which you can then threshold in fslmaths. This >> program can also give you the table listing the clusters. >> >> Cheers. >> >> >> >> >> On 24 Nov 2008, at 05:07, liang wang wrote: >> >> Dear FSLers, >> >> Using TBSS analysis pipeline, I got some stat images. Firstly I used p > >> 0.995 to threshold these stat images. Thus, some very clusters (e.g. 1 >> voxel) were also survived. Then we want to use cluster size (e.g. 10 voxels) >> to threshold the resulting images. Two questions need your help! >> >> 1) how to use cluster threshold to do this work in FSL software, similar >> to 3dcluster command in AFNI. >> >> 2) how to generate a table to report all clusters information in a stat >> image in FSL, not all voxel. I can get all voxel coordiates using fslmeants >> -i image --showall. >> >> Any suggestions are appreciated. >> Liang Wang >> -- >> Liang Wang, Postdoc >> Woodward Lab >> Department of Psychiatry >> University of British Columbia >> BC Mental Health & Addiction Services >> 938 West 28th Avenue >> Vancouver BC V5Z 4H4 >> Telephone: 1-604-875-2000 (ext. 4735) >> Fax: 1-604-875-3871 >> Email: [log in to unmask] >> >> >> >> --------------------------------------------------------------------------- >> Stephen M. Smith, Professor of Biomedical Engineering >> Associate Director, Oxford University FMRIB Centre >> >> FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK >> +44 (0) 1865 222726 (fax 222717) >> [log in to unmask] http://www.fmrib.ox.ac.uk/~steve<http://www.fmrib.ox.ac.uk/%7Esteve> >> >> --------------------------------------------------------------------------- >> >> >> >> -- >> Liang Wang, Postdoc >> Woodward Lab >> Department of Psychiatry >> University of British Columbia >> BC Mental Health & Addiction Services >> 938 West 28th Avenue >> Vancouver BC V5Z 4H4 >> Telephone: 1-604-875-2000 (ext. 4735) >> Fax: 1-604-875-3871 >> Email: [log in to unmask] >> > > > --------------------------------------------------------------------------- > Stephen M. Smith, Professor of Biomedical Engineering > Associate Director, Oxford University FMRIB Centre > > FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK > +44 (0) 1865 222726 (fax 222717) > [log in to unmask] http://www.fmrib.ox.ac.uk/~steve<http://www.fmrib.ox.ac.uk/%7Esteve> > --------------------------------------------------------------------------- > -- Liang Wang, Postdoc Woodward Lab Department of Psychiatry University of British Columbia BC Mental Health & Addiction Services 938 West 28th Avenue Vancouver BC V5Z 4H4 Telephone: 1-604-875-2000 (ext. 4735) Fax: 1-604-875-3871 Email: [log in to unmask]